Find loci with unexpected homozygous genotype calls for artificial heterozygotes.

Usage

find_unexp_homs(x, rp_row, dp_row, na_code = NA)

Arguments

x: A data matrix or frame with markers as columns and samples as rows.
rp_row, dp_row: An integer or character value indicating the row index or name of Parent 1 and 2.
na_code: A value indicating missing data in x.

Value

A list object with the following components: 1) data frame of loci with unexpected genotype calls artificial heterozygotes if present. 2) data frame of loci with expected genotype calls for artificial heterozygotes.

Details

Artificial heterozygotes are expected to show heterozygosity at polymorphic loci between parents.Use this wrapper function to detect loci which did not follow this prediction.

Examples

# example code
library(panGenomeBreedr)
# Marker data
dat <- data.frame(snp1 = c('C:C', 'A:A', 'C:A', 'C:A'),
                  snp2 = c('C:C', '-:-', 'C:C', 'C:C'),
                  snp3 = c('T:T', 'C:C', 'C:T', 'C:T'),
                  snp4 = c('G:G', '-:-', 'G:-', 'G:G'),
                  snp5 = c('T:T', 'A:A', 'T:A', 'T:A'),
                  row.names = c('rp', 'dp', 'art_het1', 'art_het2'))

# Check for unexpected homozygous genotypes
homs_unexp <- find_unexp_homs(x = dat,
                              rp_row = 1,
                              dp_row = 2)$geno_unexp